Food systems and food products are rapidly evolving, as are the associated safety challenges. In addition, our adversaries in the food safety battle are among the fastest-growing, most quickly evolving organisms known to man — E. coli, for example, can double in as little as twenty minutes.
As part of this arms race, there is a need for improved methods and tools to rapidly and reliably identify, detect, and predict food safety hazards. Next generation sequencing methods represent a new tool box that has a number of potentially transformational food safety applications, including, but not limited to whole genome sequencing (WGS). While the academic and the public sector are working to adopt and improve these new methods for food safety applications, there is a need for more members of industry to join the conversation.
Before WGS, the best method for detecting and tracing foodborne disease outbreaks and contamination events was pulsed-field gel electrophoresis, or PFGE. PFGE had an enormous positive impact on food safety after its widespread adoption in the late 1990s. For example, in the United States PFGE detects two to three listeriosis outbreaks each year, up from one outbreak every three years in the pre-PFGE 1980s.
This success is due in large part to Pulsenet, an international network of laboratories that tracks PFGE fingerprints of various foodborne pathogens, obtained from clinical specimens as well as environmental and food samples.
However, WGS offers far more powerful subtype characterization than PFGE, thanks to characterisation of nearly all the bacterial DNA. With the help of comprehensive laboratory networks, rapidly expanding WGS databases, and epidemiological data, WGS can detect foodborne disease outbreaks and trace pathogen sources along the global food chain with unprecedented resolution.
Based on the impact of WGS on detection of listeriosis outbreaks, I estimate that WGS-based surveillance can be 100 times better at detecting outbreaks than what was possible twenty years ago, when “DNA fingerprinting” tools were not used routinely for subtyping of foodborne pathogens. Consequently, industry needs to achieve equivalent improvements in their preventive food safety strategies in order to not increase food-safety associated business risks.1
Collaboration and open discussion between all stakeholders in the industry will help us move forward and share knowledge about this important technology. GFSC is one of the few opportunities for main players from all of the isolated corners of the food industry to come together – and that's the kind of forum that can result in real change.
Interpretation of WGS data however does have challenges.
First, while complete DNA-based characterisation may at first seem like a silver bullet, it can't necessarily trace outbreaks to a specific source. Not only is it possible for isolates from different sources to appear virtually identical down to the minute genetic level, isolates can also rapidly accumulate changes in their genetic materials, particularly if they are in environments where they grow rapidly.2 Hence, in basically all types of food safety related applications of WGS, epidemiological data, including data about supply-chain details, such as transportation, are needed to help accurately interpret WGS findings.
Next there’s the all-important question of cost. WGS generally is still a more expensive than PFGE, including due to the costs associated with WGS data analysis. These costs will decrease as bioinformatic tools develop mature. While some have cited costs of sequencing a full genome of a Salmonella or Listeria isolate of about 50 USD, which is less than typically charged for PFGE.3 WGS costs this low are not typically commercial available and require considerable economy of scale (e.g., sequencing of 96 isolates at one time). However, I predict that WGS of a bacterial isolates at costs of around $50 will become available over the next three to five years, particularly with some of the newer sequencing technologies.
Global public health and food regulatory agencies — including the Food and Drug Administration of the United States, the US Center of Disease Control, and the Food Standards Agency of the United Kingdom4 — are already developing the networks and databases necessary for full utilisation of WGS. The U.S. FDA is leading the charge with their GenomeTrakr network, which is billed as "the first distributed network of laboratories to utilise whole genome sequencing for pathogen identification”.5 The GenomeTrakr laboratories, located not only in the U.S. but also in Europe and Australia, collect genomic and geographic data from foodborne pathogens and house them on public databases at the National Center for Biotechnology Information that any person can access.6 Although these databases are a public resource, private industry has been slow to exploit or even become aware of them. Academia may be able to serve as the bridge between private businesses and the public agencies poised to help.
My own institution, Cornell University, has long exemplified industry-academia collaboration in food safety. Soon after PulseNet was created in 1996, Cornell's New York State College of Agriculture and Life Sciences opened the Laboratory for Molecular Typing (LMT), a fee-for-service facility for companies that want to take advantage of these technologies, including PFGE and WGS.7
I'll be discussing the topic of WGS along with the benefits and challenges it brings to food safety at this year’s Global Food Safety Conference in Tokyo. I’ll also be discussing other recent innovations during the session titled Emerging Technologies in the Food Industry – New Horizons, Challenges & Opportunities.
During the conference session, I hope to address an audience that draws from the public and private sectors as well as academia. This interdisciplinary audience may also help me refine some of my thinking about the future of WGS and other next gen sequencing tools in food safety and quality.
For example, should we sequence everything, or hone into more specific targets? How can we use this technology to prevent outbreaks rather than merely reacting to them? Even as the director of a lab that routinely performs WGS for research and industry, I don’t have all the answers. Collaboration and open discussion between all stakeholders in the industry will help us move forward and share knowledge about this important technology. GFSC is one of the few opportunities for main players from all of the isolated corners of the food industry to come together – and that's the kind of forum that can result in real change.
This post was written and contributed by:
Gellert Family Professor in Food Safety,
Cornell University, USA